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Each CpG site has a typical methylation level, with a small amount of variation between individuals.
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(c) The methylation level of individual cytosine in "CACGTG" (the typical E-box binding site of the BMAL1-CLOCK complex34), and their distance to the nearest transcriptional start site (TSS) in the ChIPed DNA from HEK-293T cells.
Distinctive class labels were low methylation (LM: methylation level ≤20%) and high methylation (HM: methylation level ≥80%) for CGIs.
To evaluate the methylation level, we calculated the percentage of methylated sites of all the CpG sites in each bin-pair, termed methylation density.
Briefly, because a CHG and CHH methylation depletion is typical for gbM genes (Bewick and Schmitz 2017), genes which had a significantly higher CHG and/or CHH DNA methylation level than the genomic average (P value <0.05) were labelled highly methylated non-gbM genes (Takuno and Gaut 2012 and Takuno et al. 2017) and excluded from further analyses.
Among unicellular organisms, kinetoplastids are unmethylated, while alveolate protists are generally methylated (Fig. 2) with secondary loss of methylation that can lead to weaker methylation level or mosaic methylation.
Average methylation level was calculated using the methylKit software package.
The DNA methylation level was calculated as 5mdC/ dC + 5mdC) × 100%.
The average methylation level in each stage was the mean of the methylation levels of each 500 bp tile.
The methylation level of each CpG is shown for the indicated cells.
Liquid chromatography/tandem mass spectrometry was used to examine leukocyte genomic DNA methylation level.
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